2-189859831-C-T

Position:

• chr2-189859831-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000534.5(PMS1):​c.1857-3912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,988 control chromosomes in the GnomAD database, including 5,142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (5142 hom., cov: 32)
• Consequence: PMS1 NM_000534.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

Genes affected

PMS1 (HGNC:9121): (PMS1 homolog 1, mismatch repair system component) This gene encodes a protein belonging to the DNA mismatch repair mutL/hexB family. This protein is thought to be involved in the repair of DNA mismatches, and it can form heterodimers with MLH1, a known DNA mismatch repair protein. Mutations in this gene cause hereditary nonpolyposis colorectal cancer type 3 (HNPCC3) either alone or in combination with mutations in other genes involved in the HNPCC phenotype, which is also known as Lynch syndrome. [provided by RefSeq, Jul 2008]

LOC105373796 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMS1	NM_000534.5	c.1857-3912C>T		intron_variant		ENST00000441310.7	NP_000525.1
LOC105373796	XR_001739151.2	n.318+2128G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PMS1	ENST00000441310.7	c.1857-3912C>T		intron_variant		1	NM_000534.5	ENSP00000406490	P1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28039 AN: 151870 Hom.: 5132 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.185 AC: 28090 AN: 151988 Hom.: 5142 Cov.: 32 AF XY: 0.182 AC XY: 13488 AN XY: 74298

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.0864

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0783 Hom.: 350

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs256571; hg19: chr2-190724557;